Align Aspartate--tRNA(Asp/Asn) ligase; Aspartyl-tRNA synthetase; AspRS; Non-discriminating aspartyl-tRNA synthetase; ND-AspRS; EC 6.1.1.23 (characterized)
to candidate WP_068176577.1 HTA01S_RS24210 aspartate--tRNA ligase
Query= SwissProt::Q51422 (591 letters) >NCBI__GCF_001592305.1:WP_068176577.1 Length = 600 Score = 733 bits (1891), Expect = 0.0 Identities = 373/591 (63%), Positives = 449/591 (75%), Gaps = 8/591 (1%) Query: 2 MRSHYCGQLNESLDGQEVTLCGWVHRRRDHGGVIFLDVRDREGLAQVVFDPDRAETFAKA 61 MRSHYCG + E+L GQ V LCGWV+RRRDHGGVIF+D+RDREG QVV DPDRAE F A Sbjct: 3 MRSHYCGLVTEALLGQTVQLCGWVNRRRDHGGVIFIDLRDREGYVQVVCDPDRAEMFKTA 62 Query: 62 DRVRSEFVVKITGKVRLRPEGARNPNMASGSIEVLGYELEVLNQAETPPFPLDEYSDVGE 121 + VR+E+ V++TG VR RPEG N N+ SG IE+L +EL+VLN + TPPF LD+ ++ E Sbjct: 63 EDVRNEYCVQVTGLVRARPEGTTNDNLKSGKIEILCHELKVLNASVTPPFQLDD-DNLSE 121 Query: 122 ETRLRYRFIDLRRPEMAAKLKLRARITSSIRRYLDDNGFLDVETPILGRPTPEGARDYLV 181 TRL +R +DLRRP M L LR R+ +R++LD NGF+D+ETP+L + TPEGARDYLV Sbjct: 122 TTRLTHRVLDLRRPYMQNNLMLRYRVAMEVRKFLDANGFIDIETPMLTKSTPEGARDYLV 181 Query: 182 PSRTYPGHFFALPQSPQLFKQLLMVAGFDRYYQIAKCFRDEDLRADRQPEFTQIDIETSF 241 PSR + GHFFALPQSPQLFKQLLMVAGFDRYYQI KCFRDEDLRADRQPEFTQIDIETSF Sbjct: 182 PSRVHDGHFFALPQSPQLFKQLLMVAGFDRYYQITKCFRDEDLRADRQPEFTQIDIETSF 241 Query: 242 LDESDIIGITEKMVRQLFKEVLDVEFDEFPHMPFEEAMRRYGSDKPDLRIPLELVDVADQ 301 L E DI + + M++ +F+ L V+ EFP M + EAM R+GSDKPDLR+ LE ++ D Sbjct: 242 LTEEDIRDMFQGMIKTVFQNTLGVDLGEFPVMAYSEAMHRFGSDKPDLRVKLEFTELTDV 301 Query: 302 LKEVEFKVFSGPANDPKGRVAALRVPGAASMPRSQIDDYTKFVGIYGAKGLAYIKVNERA 361 + +V+FKVFS PA GRV AL V G A + RS+ID YT+FV IYGAKGLA+IKVNE A Sbjct: 302 MADVDFKVFSAPATMKNGRVVALCVRGGAEISRSEIDAYTEFVKIYGAKGLAWIKVNEVA 361 Query: 362 KGVEGLQSPIVKFIPEANLNVILDRVGAVDGDIVFFGADKAKIVCDALGALRIKVGHD-- 419 KG +GLQSPIVK + +A + IL R GA DGDI+FFGADK KIV DA+GALR+K+GH Sbjct: 362 KGRDGLQSPIVKNLHDAAVAEILKRTGAQDGDIIFFGADKEKIVNDAIGALRLKIGHSEL 421 Query: 420 ---LKLLTREWAPMWVVDFPMFEENDDGS-LSALHHPFTSPKCTPAE-LEANPGAALSRA 474 L WAPMWVVDFPMFE +D+ +A+HHPFT+PK + + P +++ Sbjct: 422 GKKNGLFEARWAPMWVVDFPMFEHDDEADRWTAVHHPFTAPKDGHEDWMVTAPEKCIAKG 481 Query: 475 YDMVLNGTELGGGSIRIHDKSMQQAVFRVLGIDEAEQEEKFGFLLDALKYGAPPHGGLAF 534 YDMVLNG E+GGGS+RIH ++QQ VF L I E + KFGFLLDAL+YGAPPHGGLAF Sbjct: 482 YDMVLNGWEIGGGSVRIHTAAVQQKVFDALKITPEEAQVKFGFLLDALQYGAPPHGGLAF 541 Query: 535 GLDRLVMLMTGASSIREVIAFPKTQSAGDVMTQAPGSVDGKALRELHIRLR 585 GLDR+V LMTGA SIR+VIAFPKTQ A ++TQAP VD K LRELHIRLR Sbjct: 542 GLDRIVTLMTGAESIRDVIAFPKTQRAQCLLTQAPSLVDEKQLRELHIRLR 592 Lambda K H 0.321 0.140 0.411 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1084 Number of extensions: 45 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 591 Length of database: 600 Length adjustment: 37 Effective length of query: 554 Effective length of database: 563 Effective search space: 311902 Effective search space used: 311902 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory